We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of freedom to correctly sample the canonical distribution in a simulation of rigid molecules. We propose simple, quasisymplectic second-order numerical integrators and test their performance on the TIP4P model of water. We also investigate the optimal choice of thermostat parameters.

We propose a control scheme for selecting populations of molecular rotational states by wave-packet interference. A series of coherent rotational wave packets is created by nonadiabatic rotational excitation of molecules using two strong femtosecond laser pulses. By adjusting the time delay between the two laser pulses, constructive or destructive interference among these wave packets enables the population to be enhanced or suppressed for a specific rotational state. The evolution of the rotational wave packet with selected populations produces interference patterns with controlled spatial symmetries. This method provides an approach to prepare a molecular ensemble with selected quantum-state distributions and controlled spatial distributions under field-free condition.

Using femtosecondtime-resolved photoelectron imaging, electron-hole pairs are created in size-selected anion clusters , and the subsequent decay dynamics are measured. These clusters eject electrons via Auger decay on time scales of 100–600 fs. There is an abrupt increase in the Auger decay time for clusters larger than , coinciding with the onset of the transition from van der Waals to covalent bonding in mercury clusters. Our results also show evidence for subpicosecond excited state relaxation attributed to inelastic electron-electron and electron-hole scattering as well as hole-induced contraction of the cluster.

H atoms in are rearranged by strong optical fields generated by intense 9.3 fs laser pulses to form . This atomic rearrangement is ultrafast: It occurs within a single laser pulse. Quantum-chemical calculations reveal that originates in the state of when the O–H bond elongates to 1.15 a.u. and the H–O–H angle becomes 120°. Bond formation on the ultrafast time scale of molecular vibrations (10 fs for ) and in strong fields has hitherto not been reported.

IR-dip spectra in the NH stretch regions have been measured for the state of the indole/N-methylacetamide 1:1 clusters (Ind-). We identified two structural isomers of Ind- that possess an hydrogen bond. The redshifts of the NH stretch fundamental of the indole moieties in Ind- are larger than that for Ind- [Carney, Hagemeister, and Zweir, J. Chem. Phys.108, 3379 (1998)], indicating that the strength of the hydrogen bond in Ind- is stronger than that of the hydrogen bond in Ind-. On the basis of the natural bond orbital analysis we suggest that two lone pair orbitals of the O atoms in the NMA moiety form a dual hydrogen bond with the NH group designated by . Owing to the dual nature of the hydrogen bond its strength in Ind- is larger than that of the hydrogen bond in Ind-.

We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of freedom to correctly sample the canonical distribution in a simulation of rigid molecules. We propose simple, quasisymplectic second-order numerical integrators and test their performance on the TIP4P model of water. We also investigate the optimal choice of thermostat parameters.

For a system which undergoes electron or energy transfer in a polar solvent, we define the diabatic states to be the initial and final states of the system, before and after the nonequilibrium transfer process. We consider two models for the system-solvent interactions: A solvent which is linearly polarized in space and a solvent which responds linearly to the system. From these models, we derive two new schemes for obtaining diabatic states from ab initio calculations of the isolated system in the absence of solvent. These algorithms resemble standard approaches for orbital localization, namely, the Boys and Edmiston–Ruedenberg (ER) formalisms. We show that Boys localization is appropriate for describing electron transfer [Subotnik et al., J. Chem. Phys.129, 244101 (2008)] while ER describes both electron and energy transfer. Neither the Boys nor the ER methods require definitions of donor or acceptor fragments and both are computationally inexpensive. We investigate one chemical example, the case of oligomethylphenyl-3, and we provide attachment/detachment plots whereby the ER diabatic states are seen to have localized electron-hole pairs.

Dissipative particle dynamics (DPD) is an effective mesoscopic particle model with a lower computational cost than molecular dynamics because of the soft potentials that it employs. However, the soft potential is not strong enough to prevent the DPD particles that are used to represent the fluid from penetrating solid boundaries represented by stationary DPD particles. A phase-field variable, , is used to indicate the phase at point and time , with a smooth transition from −1 (phase 1) to (phase 2) across the interface. We describe an efficient implementation of no-slip boundary conditions in DPD models that combines solid-liquid particle-particle interactions with reflection at a sharp boundary located with subgrid scale accuracy using the phase field. This approach can be used for arbitrarily complex flow geometries and other similar particle models (such as smoothed particle hydrodynamics), and the validity of the model is demonstrated by DPD simulations of flow in confined systems with various geometries.

A multireference composite method that is based on the correlation consistent Composite Approach (ccCA) is introduced. The developed approach, multireference ccCA, has been utilized to compute the potential energy surfaces (PESs) of and , which provide rigorous tests for multireference composite methods due to the large multireference character that must be correctly described as the molecules dissociate. As well, PESs provide a stringent test of a composite method because all components of the method must work in harmony for an appropriate, smooth representation across the entire surface.

To overcome the pseudoergodicity problem, conformational sampling can be accelerated via generalized ensemble methods, e.g., through the realization of random walks along prechosen collective variables, such as spatial order parameters, energy scaling parameters, or even system temperatures or pressures, etc. As usually observed, in generalized ensemble simulations, hidden barriers are likely to exist in the space perpendicular to the collective variable direction and these residual free energy barriers could greatly abolish the sampling efficiency. This sampling issue is particularly severe when the collective variable is defined in a low-dimension subset of the target system; then the “Hamiltonian lagging” problem, which reveals the fact that necessary structural relaxation falls behind the move of the collective variable, may be likely to occur. To overcome this problem in equilibrium conformational sampling, we adopted the orthogonal space random walk (OSRW) strategy, which was originally developed in the context of free energy simulation [L. Zheng, M. Chen, and W. Yang, Proc. Natl. Acad. Sci. U.S.A.105, 20227 (2008)]. Thereby, generalized ensemble simulations can simultaneously escape both the explicit barriers along the collective variable direction and the hidden barriers that are strongly coupled with the collective variable move. As demonstrated in our model studies, the present OSRW based generalized ensemble treatments show improved sampling capability over the corresponding classical generalized ensemble treatments.

The method of extracting effective atomic orbitals and effective minimal basis sets from molecular wave function characterizing the state of an atom in a molecule is developed in the framework of the “fuzzy” atoms. In all cases studied, there were as many effective orbitals that have considerable occupation numbers as orbitals in the classical minimal basis. That is considered to be of high conceptual importance.

The quantum-classical correspondence in the presence of dissipation is studied. The semiclassical expression for the linear response function of an anharmonic system is expressed in a series containing classical stability matrix elements, which can diverge due to the chaotic behavior of stochastic trajectories. The presence of dissipation in most cases removes the divergence of higher-order correction terms, thus suppressing quantum effects and making the system more classical. The regime of system-bath coupling, which makes quantum dynamics completely classical, is obtained in terms of friction, temperature, and anharmonicity. Special cases when bath coupling may lead to enhancement of quantum effects are discussed.

The quasidiabatic, coupled electronic state, fully quadratic Hamiltonian , suitable for the simulation of spectra exhibiting strong vibronic couplings and constructed using a recently introduced pseudonormal equations approach, is studied. The flexibility inherent in the normal equations approach is shown to provide a robust means for (i) improving the accuracy of , (ii) extending its domain of utility, and (iii) determining the limits of the fully quadratic model. The two lowest electronic states of pyrrolyl which are coupled by conical intersections are used as a test case. The requisite ab initio data are obtained from large multireference configuration interaction expansions comprised of configuration state functions and based on polarized triple zeta quality atomic orbital bases.

Based on a microscopic Hamiltonian picture where the system is coupled with the nonequilibrium environment, comprising of a set of harmonic oscillators, the Langevin equation with proper microscopic specification of Langevin force is formulated analytically. In our case, the reservoir is perturbed by an external force, either executing rapid or showing periodic fluctuations, hence the reservoir is not in thermal equilibrium. In the presence of external fluctuating force, using Shapiro–Loginov procedure, we arrive at the linear coupled first order differential equations for the two-time correlations and examine the time evolution of the same considering the system as a simple harmonic oscillator. We study the stochastic resonance phenomena of a Kubo-type oscillator (assumed to be the system) when the bath is modulated by a periodic force. The result(s) obtained here is of general significance and can be used to analyze the signature of stochastic resonance.

The observation of long-lived electronic coherence in photosynthetic excitation energy transfer (EET) by Engel et al. [Nature (London)446, 782 (2007)] raises questions about the role of the protein environment in protecting this coherence and the significance of the quantum coherence in light harvesting efficiency. In this paper we explore the applicability of the Redfield equation in its full form, in the secular approximation and with neglect of the imaginary part of the relaxation terms for the study of these phenomena. We find that none of the methods can give a reliable picture of the role of the environment in photosynthetic EET. In particular the popular secular approximation (or the corresponding Lindblad equation) produces anomalous behavior in the incoherent transfer region leading to overestimation of the contribution of environment-assisted transfer. The full Redfield expression on the other hand produces environment-independent dynamics in the large reorganization energy region. A companion paper presents an improved approach, which corrects these deficiencies [A. Ishizaki and G. R. Fleming, J. Chem. Phys.130, 234111 (2009)].

A new quantum dynamic equation for excitation energy transfer is developed which can describe quantum coherent wavelike motion and incoherent hopping in a unified manner. The developed equation reduces to the conventional Redfield theory and Förster theory in their respective limits of validity. In the regime of coherent wavelike motion, the equation predicts several times longer lifetime of electronic coherence between chromophores than does the conventional Redfield equation. Furthermore, we show quantum coherent motion can be observed even when reorganization energy is large in comparison to intersite electronic coupling (the Förster incoherent regime). In the region of small reorganization energy, slow fluctuation sustains longer-lived coherent oscillation, whereas the Markov approximation in the Redfield framework causes infinitely fast fluctuation and then collapses the quantum coherence. In the region of large reorganization energy, sluggish dissipation of reorganization energy increases the time electronic excitation stays above an energy barrier separating chromophores and thus prolongs delocalization over the chromophores.

Short-range DFT/long-range ab initio methods allow for a combination of the weak basis-set dependency of DFT with an accurate ab initio treatment of long-range effects like van der Waals interaction. In order to improve existing short-range LDA and GGA density functionals, we developed a TPSS-like short-range meta-GGA exchange-correlation functional and checked its performance in long-range CCSD(T) calculations for thermodynamical properties of the G2 set of molecules.

A multiple coherent states implementation of the semiclassical approximation is introduced and employed to obtain the power spectra with a few classical trajectories. The method is integrated with the time-averaging semiclassical initial value representation to successfully reproduce anharmonicity and Fermi resonance splittings at a level of accuracy comparable to semiclassical simulations of thousands of trajectories. The method is tested on two different model systems with analytical potentials and implemented in conjunction with the first-principles molecular dynamics scheme to obtain the power spectrum for the carbon dioxide molecule.

This article presents an efficient and parallelized implementation of the density matrix renormalization group (DMRG) algorithm for quantum chemistry calculations. The DMRG method as a large-scale multireference electronic structure model is by nature particularly efficient for one-dimensionally correlated systems, while the present development is oriented toward applications for polynuclear transition metal compounds, in which the macroscopic one-dimensional structure of electron correlation is absent. A straightforward extension of the DMRG algorithm is proposed with further improvements and aggressive optimizations to allow its application with large multireference active space, which is often demanded for metal compound calculations. Special efficiency is achieved by making better use of sparsity and symmetry in the operator and wave function representations. By accomplishing computationally intensive DMRG calculations, the authors have found that a large number of renormalized basis states are required to represent high entanglement of the electron correlation for metal compound applications, and it is crucial to adopt auxiliary perturbative correction to the projected density matrix during the DMRG sweep optimization in order to attain proper convergence to the solution. Potential energy curve calculations for the molecule near the known equilibrium precisely predicted the full configuration interaction energies with a correlation space of 24 electrons in 30 orbitals [denoted by ]. The energies are demonstrated to be accurate to (the error from the extrapolated best value) when as many as 10 000 renormalized basis states are employed for the left and right DMRG block representations. The relative energy curves for along the isomerization coordinate were obtained from DMRG and other correlated calculations, for which a fairly large orbital space is modeled as a full correlation space. The DMRG prediction nearly overlaps with the energy curve from the coupled cluster with singles, doubles, and perturbative triple [CCSD(T)] calculations, while the multireference complete active space self-consistent field (CASSCF) calculations with the small reference configuration are found to overestimate the biradical character of the electronic state of according to the one-electron density matrix analysis.

In spite of its success in molecular dynamics and the advantage of being a first order propagation technique, the Car–Parrinello method and its variations have not been successful in self-consistent-field (SCF) wave functionoptimization due to slow convergence. In this article, we introduce a first principles fictitious mass scheme to weigh each individual density element differently and instantaneously. As an alternative to diagonalization in SCF, the Car–Parrinello scheme is implemented as a density matrix search method. Not only does the fictitious mass scheme developed herein allow a very fast SCF convergence, but also the Car–Parrinello density matrix search (CP-DMS) exhibits linear scaling with respect to the system size for alanine helical chain test molecules. The excellent performance of CP-DMS holds even for very challenging compact three-dimensional quantum particles. While the conventional diagonalization based SCF method has difficulties optimizing electronic wave functions for CdSequantum dots, CP-DMS shows both smooth and faster convergence.